Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Russia. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively (see Methods or our paper for further explanation).
Using data available up to the: 2020-06-18
Note that it takes time for infection to cause symptoms, to get tested for SARS-CoV-2 infection, for a positive test to return and ultimately to enter the case data presented here. In other words, today’s case data are only informative of new infections about two weeks ago. This is reflected in the plots below, which are by date of infection.
Figure 1: The results of the latest reproduction number estimates (based on estimated confirmed cases with a date of infection on the 2020-05-12) in Russia, stratified by region, can be summarised by whether confirmed cases are likely increasing or decreasing. This represents the strength of the evidence that the reproduction number in each region is greater than or less than 1, respectively (see the methods for details). Regions with fewer than 40 confirmed cases reported on a single day are not included in the analysis (light grey).
| Estimate | |
|---|---|
| New confirmed cases by infection date | 9099 (8499 – 9619) |
| Expected change in daily cases | Increasing |
| Effective reproduction no. | 1 (1 – 1.1) |
| Doubling/halving time (days) | 79 (49 – 190) |
| Adjusted R-squared | 0.78 (0.58 – 0.98) |
Figure 2: A.) Confirmed cases by date of report (bars) and their estimated date of infection. B.) Time-varying estimate of the effective reproduction number. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Estimates from existing data are shown up to the 2020-05-12 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.
Figure 3: A.) Time-varying estimate of the rate of growth, B.) Time-varying estimate of the doubling time in days (when negative this corresponds to the halving time), C.) The adjusted R-squared estimates indicating the goodness of fit of the exponential regression model (with values closer to 1 indicating a better fit). Estimates from existing data are shown up to the 2020-05-12. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.
Figure 4: Confirmed cases with date of infection on the 2020-05-12 and the time-varying estimate of the effective reproduction number (light bar = 90% credible interval; dark bar = the 50% credible interval.). Regions are ordered by the number of expected daily confirmed cases and shaded based on the expected change in daily confirmedcases. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control and a single case required for elimination.
Figure 5: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates from existing data are shown up to the 2020-05-12 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control. The vertical dashed line indicates the date of report generation.
Figure 6: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates from existing data are shown up to the 2020-05-12 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.
Figure 7: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates from existing data are shown up to the 2020-05-12 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control. The vertical dashed line indicates the date of report generation.
Figure 8: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates from existing data are shown up to the 2020-05-12 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.
| Region | New confirmed cases by infection date | Expected change in daily cases | Effective reproduction no. | Doubling/halving time (days) |
|---|---|---|---|---|
| Adygea Republic | 41 (28 – 53) | Increasing | 1.4 (1 – 1.7) | 8.3 (4.6 – 48) |
| Altai Krai | 50 (37 – 62) | Likely increasing | 1.2 (0.9 – 1.4) | 16 (6.8 – -46) |
| Altayskiy kray | 51 (38 – 64) | Likely increasing | 1.2 (0.9 – 1.4) | 16 (6.8 – -51) |
| Arkhangelsk oblast | 44 (32 – 58) | Likely increasing | 1.1 (0.9 – 1.4) | 22 (7.4 – -22) |
| Arkhangelsk Oblast | 44 (29 – 56) | Likely increasing | 1.1 (0.9 – 1.4) | 21 (7.4 – -23) |
| Astrahan oblast | 46 (32 – 57) | Unsure | 1 (0.8 – 1.2) | 92 (10 – -14) |
| Astrakhan Oblast | 46 (32 – 57) | Unsure | 1 (0.8 – 1.2) | 140 (11 – -13) |
| Bashkortostan Republic | 92 (75 – 109) | Unsure | 1.1 (0.9 – 1.2) | 44 (12 – -27) |
| Belgorod oblast | 73 (56 – 87) | Unsure | 1.1 (0.9 – 1.2) | 65 (13 – -20) |
| Belgorod Oblast | 74 (58 – 87) | Unsure | 1.1 (0.9 – 1.2) | 55 (12 – -21) |
| Briansk oblast | 107 (87 – 124) | Likely increasing | 1.1 (1 – 1.3) | 19 (9.3 – -210) |
| Bryansk Oblast | 106 (88 – 123) | Likely increasing | 1.1 (1 – 1.3) | 19 (9.2 – -260) |
| Buryatia Republic | 43 (29 – 53) | Unsure | 1 (0.8 – 1.2) | 220 (11 – -12) |
| Chechen republic | 25 (13 – 33) | Unsure | 1 (0.7 – 1.2) | -81 (10 – -8.1) |
| Chechen Republic | 25 (14 – 33) | Unsure | 1 (0.7 – 1.3) | -90 (9.8 – -7.9) |
| Cheliabinsk oblast | 85 (69 – 101) | Likely increasing | 1.1 (0.9 – 1.2) | 44 (12 – -26) |
| Chelyabinsk Oblast | 86 (69 – 103) | Likely increasing | 1.1 (0.9 – 1.2) | 43 (12 – -26) |
| Chuvashia Republic | 84 (67 – 99) | Unsure | 1.1 (0.9 – 1.2) | 50 (13 – -24) |
| Dagestan Republic | 97 (78 – 113) | Unsure | 1 (0.8 – 1.1) | -120 (21 – -15) |
| Habarovskiy kray | 57 (42 – 70) | Likely increasing | 1.1 (0.9 – 1.3) | 27 (8.8 – -25) |
| Hanty-Mansiyskiy AO | 74 (55 – 88) | Likely increasing | 1.1 (0.9 – 1.3) | 28 (9.8 – -33) |
| Ingushetia republic | 43 (32 – 55) | Unsure | 1 (0.8 – 1.2) | 300 (11 – -12) |
| Ingushetia Republic | 43 (29 – 54) | Unsure | 1 (0.8 – 1.2) | 330 (11 – -12) |
| Irkutsk oblast | 61 (46 – 74) | Increasing | 1.3 (1 – 1.5) | 10 (5.6 – 54) |
| Irkutsk Oblast | 60 (47 – 74) | Increasing | 1.3 (1 – 1.5) | 10 (5.7 – 62) |
| Ivanovo oblast | 53 (37 – 65) | Unsure | 1 (0.7 – 1.1) | -31 (24 – -9.5) |
| Ivanovo Oblast | 52 (37 – 64) | Unsure | 0.9 (0.7 – 1.1) | -31 (24 – -9.6) |
| Kabardino-Balkarian Republic | 69 (51 – 83) | Unsure | 1 (0.8 – 1.1) | -69 (20 – -12) |
| Kaliningrad oblast | 36 (24 – 45) | Unsure | 1 (0.8 – 1.3) | 120 (9.7 – -12) |
| Kaliningrad Oblast | 36 (25 – 46) | Unsure | 1 (0.8 – 1.3) | 140 (10 – -12) |
| Kalmykia Republic | 30 (20 – 39) | Unsure | 1 (0.8 – 1.3) | 160 (9.5 – -11) |
| Kaluga oblast | 113 (93 – 130) | Likely increasing | 1.1 (0.9 – 1.2) | 34 (12 – -42) |
| Kaluga Oblast | 113 (92 – 127) | Likely increasing | 1.1 (0.9 – 1.2) | 36 (13 – -41) |
| Kamchatka Krai | 21 (11 – 29) | Likely increasing | 1.2 (0.9 – 1.6) | 14 (5 – -16) |
| Kamchatskiy kray | 21 (10 – 28) | Likely increasing | 1.2 (0.8 – 1.6) | 15 (4.9 – -14) |
| Karachay-Cherkess Republic | 17 (8 – 25) | Unsure | 1 (0.7 – 1.4) | 4300 (7.4 – -7.5) |
| Khabarovsk Krai | 57 (43 – 71) | Likely increasing | 1.1 (0.9 – 1.3) | 27 (8.9 – -26) |
| Khakassia Republic | 29 (17 – 38) | Unsure | 1.1 (0.8 – 1.3) | 98 (8.5 – -10) |
| Khanty-Mansi Autonomous Okrug | 74 (57 – 88) | Likely increasing | 1.1 (0.9 – 1.3) | 28 (9.6 – -33) |
| Kirov oblast | 33 (21 – 42) | Unsure | 1.1 (0.8 – 1.3) | 56 (8.1 – -12) |
| Kirov Oblast | 33 (22 – 42) | Unsure | 1.1 (0.8 – 1.3) | 64 (8.5 – -12) |
| Komi republic | 27 (16 – 36) | Likely increasing | 1.2 (0.9 – 1.5) | 12 (5 – -26) |
| Komi Republic | 27 (17 – 35) | Likely increasing | 1.2 (0.9 – 1.5) | 13 (5.1 – -23) |
| Krasnodar Krai | 94 (75 – 109) | Unsure | 1 (0.9 – 1.1) | -170 (19 – -16) |
| Krasnodarskiy kray | 94 (75 – 110) | Unsure | 1 (0.9 – 1.1) | -170 (20 – -16) |
| Krasnoyarsk Krai | 201 (170 – 229) | Increasing | 1.4 (1.2 – 1.5) | 8.7 (6.2 – 14) |
| Krasnoyarskiy kray | 201 (169 – 228) | Increasing | 1.4 (1.2 – 1.5) | 8.8 (6.2 – 15) |
| Kursk oblast | 82 (63 – 96) | Unsure | 1.1 (0.9 – 1.2) | 58 (13 – -23) |
| Kursk Oblast | 81 (65 – 98) | Unsure | 1 (0.9 – 1.2) | 58 (12 – -23) |
| Leningrad Oblast | 70 (54 – 84) | Unsure | 1 (0.9 – 1.2) | -990 (15 – -15) |
| Leningradskaya oblast | 71 (53 – 85) | Unsure | 1 (0.8 – 1.2) | 590 (15 – -15) |
| Lipetsk oblast | 61 (46 – 73) | Likely increasing | 1.1 (0.9 – 1.3) | 27 (9.3 – -27) |
| Lipetsk Oblast | 62 (45 – 74) | Likely increasing | 1.1 (0.9 – 1.3) | 25 (8.9 – -28) |
| Magadan oblast | 9 (2 – 15) | Likely increasing | 1.4 (0.7 – 2) | 8.1 (2.8 – -9.5) |
| Magadan Oblast | 9 (3 – 16) | Likely increasing | 1.4 (0.7 – 2) | 7.9 (2.8 – -9.5) |
| Mari El Republic | 47 (32 – 59) | Likely increasing | 1.1 (0.9 – 1.3) | 22 (7.6 – -23) |
| Mordovia Republic | 35 (23 – 46) | Unsure | 1 (0.8 – 1.2) | -120 (11 – -9.2) |
| Moscow | 3565 (3387 – 3757) | Decreasing | 0.9 (0.8 – 0.9) | -18 (-23 – -14) |
| Moscow oblast | 947 (877 – 1027) | Unsure | 1 (1 – 1.1) | -350 (64 – -47) |
| Moscow Oblast | 946 (869 – 1032) | Unsure | 1 (1 – 1.1) | -360 (62 – -46) |
| Murmansk oblast | 41 (29 – 52) | Unsure | 0.9 (0.7 – 1.2) | 48 (9.1 – -15) |
| Murmansk Oblast | 41 (30 – 52) | Unsure | 0.9 (0.7 – 1.2) | 53 (9.6 – -15) |
| Nizhegorodskaya oblast | 247 (216 – 273) | Likely decreasing | 1 (0.9 – 1) | -44 (93 – -17) |
| Nizhny Novgorod Oblast | 246 (219 – 272) | Likely decreasing | 1 (0.9 – 1) | -43 (110 – -18) |
| North Ossetia - Alania Republic | 75 (59 – 91) | Unsure | 1 (0.8 – 1.2) | 690 (15 – -16) |
| Novosibirsk oblast | 75 (59 – 91) | Unsure | 1 (0.9 – 1.2) | 99 (13 – -19) |
| Novosibirsk Oblast | 76 (60 – 92) | Unsure | 1 (0.9 – 1.2) | 95 (14 – -19) |
| Omsk oblast | 58 (44 – 72) | Increasing | 1.3 (1 – 1.5) | 11 (6 – 150) |
| Omsk Oblast | 58 (44 – 70) | Increasing | 1.3 (1 – 1.5) | 12 (6.1 – 170) |
| Orel oblast | 53 (38 – 66) | Unsure | 1 (0.8 – 1.2) | -63 (16 – -11) |
| Orel Oblast | 53 (36 – 66) | Unsure | 1 (0.8 – 1.2) | -70 (17 – -11) |
| Orenburg oblast | 42 (29 – 53) | Unsure | 1 (0.8 – 1.2) | -40 (17 – -9.4) |
| Orenburg Oblast | 43 (29 – 54) | Unsure | 1 (0.8 – 1.2) | -43 (16 – -9.3) |
| Pensa oblast | 76 (61 – 91) | Increasing | 1.2 (1 – 1.4) | 13 (6.8 – 120) |
| Penza Oblast | 76 (59 – 90) | Increasing | 1.2 (1 – 1.4) | 13 (6.9 – 130) |
| Perm Krai | 53 (39 – 66) | Likely increasing | 1.2 (0.9 – 1.4) | 14 (6.5 – -86) |
| Perm oblast | 52 (37 – 64) | Likely increasing | 1.2 (1 – 1.4) | 14 (6.5 – -84) |
| Primorskiy kray | 61 (45 – 76) | Unsure | 1.1 (0.8 – 1.2) | 49 (11 – -20) |
| Primorsky Krai | 61 (47 – 77) | Unsure | 1.1 (0.9 – 1.2) | 46 (10 – -19) |
| Republic of Adygeia | 42 (30 – 55) | Increasing | 1.4 (1 – 1.7) | 8.3 (4.6 – 47) |
| Republic of Bashkortostan | 92 (74 – 108) | Unsure | 1.1 (0.9 – 1.2) | 41 (12 – -28) |
| Republic of Buriatia | 42 (31 – 53) | Unsure | 1 (0.8 – 1.2) | 800 (12 – -12) |
| Republic of Chuvashia | 84 (69 – 101) | Unsure | 1.1 (0.9 – 1.2) | 49 (12 – -24) |
| Republic of Dagestan | 96 (78 – 112) | Unsure | 1 (0.8 – 1.1) | -89 (23 – -15) |
| Republic of Hakassia | 29 (17 – 38) | Unsure | 1.1 (0.8 – 1.3) | 93 (8.4 – -10) |
| Republic of Kabardino-Balkaria | 69 (52 – 83) | Unsure | 1 (0.8 – 1.1) | -73 (19 – -12) |
| Republic of Kalmykia | 30 (19 – 39) | Unsure | 1 (0.8 – 1.3) | 110 (9.2 – -11) |
| Republic of Karachaevo-Cherkessia | 18 (8 – 26) | Unsure | 1 (0.7 – 1.4) | 480 (7.3 – -7.5) |
| Republic of Mariy El | 47 (33 – 59) | Unsure | 1.1 (0.9 – 1.3) | 24 (7.9 – -23) |
| Republic of Mordovia | 34 (22 – 44) | Unsure | 1 (0.8 – 1.2) | -75 (12 – -9) |
| Republic of North Osetia - Alania | 75 (56 – 90) | Unsure | 1 (0.9 – 1.2) | 390 (15 – -16) |
| Republic of Tatarstan | 80 (60 – 94) | Unsure | 1 (0.8 – 1.1) | -250 (17 – -15) |
| Republic of Tyva | 47 (31 – 58) | Increasing | 1.3 (1 – 1.6) | 10 (5.4 – 150) |
| Republic of Udmurtia | 12 (4 – 17) | Unsure | 1.1 (0.7 – 1.6) | 24 (4.5 – -6.9) |
| Rostov oblast | 123 (101 – 141) | Likely increasing | 1.1 (1 – 1.3) | 21 (10 – -160) |
| Rostov Oblast | 122 (100 – 139) | Likely increasing | 1.1 (1 – 1.3) | 21 (10 – -350) |
| Ryazan oblast | 93 (74 – 109) | Unsure | 1 (0.9 – 1.1) | 870 (18 – -18) |
| Ryazan Oblast | 93 (75 – 109) | Unsure | 1 (0.9 – 1.2) | 560 (17 – -18) |
| Saha republic | 51 (37 – 63) | Unsure | 1.1 (0.9 – 1.3) | 38 (9.6 – -19) |
| Saint Petersburg | 469 (423 – 513) | Increasing | 1.1 (1 – 1.2) | 33 (18 – 190) |
| Sakha (Yakutiya) Republic | 50 (38 – 62) | Unsure | 1.1 (0.9 – 1.3) | 45 (9.9 – -18) |
| Samara oblast | 74 (58 – 88) | Unsure | 1 (0.9 – 1.2) | 150 (14 – -17) |
| Samara Oblast | 75 (60 – 91) | Unsure | 1 (0.9 – 1.2) | 100 (14 – -18) |
| Saratov oblast | 100 (80 – 117) | Unsure | 1.1 (0.9 – 1.2) | 44 (13 – -30) |
| Saratov Oblast | 99 (80 – 117) | Unsure | 1.1 (0.9 – 1.2) | 47 (12 – -27) |
| Sevastopol | 6 (1 – 11) | Unsure | 1.4 (0.5 – 2.3) | -23 (3.6 – -2.8) |
| Smolensk oblast | 55 (40 – 67) | Unsure | 1 (0.8 – 1.2) | -38 (21 – -9.9) |
| Smolensk Oblast | 56 (42 – 69) | Unsure | 1 (0.8 – 1.2) | -43 (20 – -10) |
| Stavropol Krai | 69 (52 – 82) | Likely increasing | 1.1 (0.9 – 1.3) | 26 (9.2 – -33) |
| Stavropolskiy kray | 69 (50 – 82) | Likely increasing | 1.1 (0.9 – 1.3) | 26 (9.1 – -32) |
| Sverdlov oblast | 138 (116 – 158) | Unsure | 1 (0.9 – 1.2) | 110 (18 – -25) |
| Sverdlovsk Oblast | 139 (116 – 157) | Unsure | 1 (0.9 – 1.2) | 95 (17 – -27) |
| Tambov oblast | 85 (67 – 100) | Unsure | 1 (0.9 – 1.2) | -800 (18 – -16) |
| Tambov Oblast | 84 (68 – 101) | Unsure | 1 (0.9 – 1.2) | -340 (17 – -16) |
| Tatarstan Republic | 80 (63 – 94) | Unsure | 1 (0.9 – 1.1) | -360 (17 – -16) |
| Tomsk oblast | 19 (10 – 27) | Unsure | 1 (0.7 – 1.3) | -40 (9 – -6.2) |
| Tomsk Oblast | 19 (12 – 28) | Unsure | 1 (0.7 – 1.3) | -47 (8.9 – -6.5) |
| Tula oblast | 95 (76 – 111) | Unsure | 1 (0.9 – 1.1) | 280 (16 – -19) |
| Tula Oblast | 94 (74 – 110) | Unsure | 1 (0.9 – 1.1) | 310 (17 – -19) |
| Tumen oblast | 41 (30 – 52) | Unsure | 1 (0.7 – 1.1) | -33 (18 – -8.9) |
| Tver oblast | 35 (22 – 45) | Unsure | 1.1 (0.8 – 1.3) | 48 (8.3 – -13) |
| Tver Oblast | 35 (23 – 45) | Unsure | 1.1 (0.8 – 1.3) | 51 (8.7 – -13) |
| Tyumen Oblast | 41 (29 – 52) | Unsure | 1 (0.8 – 1.2) | -35 (18 – -9) |
| Tyva Republic | 46 (33 – 56) | Increasing | 1.3 (1 – 1.6) | 11 (5.5 – 220) |
| Udmurt Republic | 11 (4 – 17) | Unsure | 1.1 (0.6 – 1.6) | 28 (4.5 – -6.7) |
| Ulianovsk oblast | 83 (63 – 97) | Likely increasing | 1.1 (1 – 1.3) | 21 (9 – -62) |
| Ulyanovsk Oblast | 83 (64 – 98) | Likely increasing | 1.1 (1 – 1.3) | 21 (8.9 – -64) |
| Vladimir oblast | 77 (61 – 92) | Unsure | 1.1 (0.9 – 1.2) | 57 (12 – -22) |
| Vladimir Oblast | 77 (60 – 93) | Unsure | 1.1 (0.9 – 1.2) | 55 (12 – -22) |
| Volgograd oblast | 83 (64 – 98) | Unsure | 1 (0.9 – 1.2) | -100 (20 – -15) |
| Volgograd Oblast | 82 (64 – 97) | Unsure | 1 (0.8 – 1.1) | -97 (20 – -14) |
| Voronezh oblast | 43 (30 – 54) | Unsure | 1 (0.8 – 1.2) | 760 (12 – -12) |
| Voronezh Oblast | 43 (30 – 54) | Unsure | 1 (0.8 – 1.2) | -1600 (12 – -12) |
| Yamalo-Nenets Autonomous Okrug | 67 (51 – 80) | Unsure | 1 (0.8 – 1.2) | 78000 (15 – -15) |
| Yamalo-Nenetskiy AO | 67 (52 – 81) | Unsure | 1 (0.8 – 1.1) | -520 (16 – -15) |
| Yaroslavl oblast | 112 (90 – 128) | Increasing | 1.1 (1 – 1.3) | 20 (9.6 – -190) |
| Yaroslavl Oblast | 112 (92 – 129) | Increasing | 1.1 (1 – 1.3) | 21 (9.8 – -170) |
| Zabaykalskiy kray | 34 (23 – 45) | Unsure | 1.1 (0.9 – 1.4) | 30 (7.6 – -15) |
| Zabaykalsky Krai | 35 (22 – 45) | Unsure | 1.1 (0.9 – 1.4) | 29 (7.5 – -16) |
Abbott, Sam, Joel Hellewell, James D. Munday, and Sebastian Funk. 2020. “NCoVUtils: Utility Functions for the 2019-Ncov Outbreak.” - - (-): –. https://doi.org/10.5281/zenodo.3635417.
Mironov, Sergey. 2020. “COVID-19 Data from Jhu Csse, Updated with Details on Russian Regions.” Github Repository. https://github.com/grwlf/COVID-19_plus_Russia.
Xu, Bo, Bernardo Gutierrez, Sarah Hill, Samuel Scarpino, Alyssa Loskill, Jessie Wu, Kara Sewalk, et al. n.d. “Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data.” http://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337.